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	<TITLE>MarvinView Help</TITLE>
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<BODY><H1>Introduction to MarvinView</H1>
<P><A HREF="view-index.html">Table of Contents</A> 
</P>

<H2><A NAME="introduction"></a>Introduction</H2>
MarvinView is a Java-based program for displaying molecular structures in 2- and 3-D.  Though MarvinView is not intended as an editing tool, it can easily open the current molecule in a MarvinSketch window and retrieve the changes made there.  MarvinView allows the user to quickly and easily control many aspects of the display, such as molecule display format, color scheme, dimension, and point of view.

<H2><A NAME="marvinview-gui"></A>MarvinView GUI Reference</H2>

<H3><A NAME="canvas"></A>Canvas</H3>
The Canvas is the viewing area for display and manipulation of molecules.  You can also change a number of display options from within the canvas, using your mouse.

<h3><a name="menubar"></a>Menu Bar</h3>
<CENTER>
	<TABLE WIDTH=450 BORDER=1 CELLPADDING=5 cellspacing="0" id="grid">
		<TR>
			<Th COLSPAN=2>
				<P ALIGN=CENTER>Menus and Major Submenus</P>
			</Th>
		</TR>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>File Menu</P>
			</TD>
			<TD>
				<P>The File menu contains the available file operations, such as
				<B class="buttonName">New,
				Open, Save, Print, and Close</B> The (unsigned)
				Swing applets contain only a subset of these functions.
						</P>
			</TD>
		</TR>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>Edit Menu</P>
			</TD>
			<TD>
				<P>The Edit menu contains general editing functionality (i.e.
				<B class="buttonName">Copy</B>
				and <B class="buttonName">Paste</B>)
				as well as Marvin-specific editing options. <BR>
				</P>
			</TD>
		</TR>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>Edit Source</P>
			</TD>
			<TD>
				<P>Choosing <B class="buttonName">Source</B>
				from the <B class="buttonName">Edit</B> menu opens the Edit Source  window.
				The Edit Source window opens the file for the current molecule as text.  You can view and edit the molecule file in any of the supported formats (SMILES, molfile, XYZ, etc).

				</P>
			</TD>
		</TR>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>View Menu</P>
			</TD>
			<TD>
				<P>The View Menu allows you to alter the display options for the
				structure.  
				 You can change the molecule display type and color
				scheme, hydrogen display options, display of atomic symbols, etc.
				</P>
			</TD>
		</TR>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>Hydrogens Submenu</P>
			</TD>
			<TD>
				<P>The Hydrogens Submenu controls the display of implicit and
				explicit hydrogen atoms in the molecule.<BR>See 
				<a href="view-basic.html#implicit-explicit-H">Hydrogen Display</a> for more information.
				</P>
			</TD>
		</TR>
		<tr valign="top">
		<td>Table</td>
		<td> &nbsp;</td>
		</tr>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>Tools</P>
			</TD>
			<TD>
	<P>See <a href="../calculations/calculator-plugins.html">Calculator Plug-ins</a>
				</P>
			</TD>
		</TR>
		<TR VALIGN=TOP>
    		<TD WIDTH=20%>
        	<P>Pages</P>
    		</TD>
    		<TD>
        	<P>See <a HREF="view-basic.html#howto-multipage"
            	>How to Work with Multipage Molecular Documents</a></P>
   	 	</TD>
		</TR>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>Help</P>
			</TD>
			<TD>
				<P>Select the <B class="buttonName">Help</B>
				menu item to access this help document. <BR><B class="buttonName">About
				Marvin</B> displays information about Marvin.
				<BR><B class="buttonName">About
				JVM</B> displays information about your
				software environment (JVM version, Operating system, Marvin's
				version).</P>
			</TD>
		</TR>
	</TABLE>
</CENTER>
<H2><A NAME="popup-menu"></A>Pop-up Menu</H2>
<P>The pop-up menu appears when you right-click on open canvas
space . 
Pop-up menu items include:</P>
<CENTER>
	<TABLE WIDTH=450 BORDER=1 CELLPADDING=5 cellspacing="0" id="grid">
	<TR>
			<Th width="30%">
				<P>Menu Item 
				</P>
			</Th>
			<Th WIDTH=70%>
				<P>Description 
				</P>
			</Th>
		</TR>
		<TR>
			<TD>
			Move
			</TD>
			<TD>
			The <B class="buttonName">Move</B> submenu contains a group of movement options.
			These options consist of <B class="buttonName">Translate or Drag</B>,<B class="buttonName">Zoom</B>, <B class="buttonName">Rotate</B>, and <B class="buttonName">Rotate in 3D</B>.  Selecting one of these items will make that type of motion the result of mouse dragging on the canvas.	
			</TD>
		</TR>
		<TR>
			<TD>
			Animation
			</TD>
			<TD>
			The Animation submenu contains options for 3D animation of the displayed molecule.
			</TD>
		</TR>
		<TR>
			<TD>
			Display
			</TD>
			<TD>
			The Display submenu contains options for changing the display format, display of atom labels, and resolution. Available display formats are
<B class="buttonName">Wireframe, Wireframe
with Knobs, Sticks, Ball and Stick,</B> and <B class="buttonName">Spacefill</B>.
You can set the resolution to low or high via the <B class="buttonName">Quality</B>
submenu. 
			</TD>
		</TR>
		<TR>
			<TD>
			Colors
			</TD>
			<TD>
			The <B class="buttonName">Colors</B> submenu allows you to specify the
                            <A HREF="../developer/sketchman.html#parameters.colorScheme">color
scheme</A> of the molecules. The available options are: 

Monochrome , CPK, Shapely, Group, and Atom Set 

			</TD>
		</TR>
		<TR VALIGN=TOP>
			<TD WIDTH=20%>
				<P>Hydrogens Submenu</P>
			</TD>
			<TD>
				<P>The <B class="buttonName">Hydrogens</B> submenu controls the display of implicit and
				explicit hydrogen atoms in the molecule.<BR>See <A HREF="view-basic.html#implicit-explicit-H">Implicit/Explicit
				Hydrogens</A> 
				</P>
			</TD>
		</TR>

		<TR>
			<TD>
			Edit
			</TD>
			<TD>
			The <B class="buttonName">Edit</B> submenu contains a copy of the Edit menu from the Menu Bar.
			</TD>
		</TR>
		<TR>
			<TD>
			Print
			</TD>
			<TD>
			Sends the molecule to the printer.
			</TD>
		</TR>
		<TR>
			<TD>
			Window
			</TD>
			<TD>
			Pops up a separate MarvinView Window.  This can be especially useful when the applet is embedded in an HTML page and the user wishes to have a separate window to work in.
			</TD>
		</TR>
	</TABLE>
</CENTER>
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<a HREF="http://www.chemaxon.com">ChemAxon Ltd.</a>
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<a HREF="http://www.chemaxon.com/marvin">http://www.chemaxon.com/marvin</a>
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